Human background DNA on stones in an urban environment.

Stones are frequently used as tools in criminal acts. In our department, around 5 % of all analysed crime scene related trace samples are contact or touch DNA traces swabbed from stones. These samples are primarily related to cases of damage to property and burglary. In court, questions can arise about DNA transfer and the persistence of background DNA not related to the respective crime. To shed some light on the question of how likely it is to detect human DNA as background DNA on stones from an urban environment, the surfaces of 108 stones sampled throughout the city of Bern, the Swiss capital, were swabbed. We detected a median quantity of 33 pg on the sampled stones. STR-profiles suitable for a CODIS (Combined DNA Index System) registration in the Swiss DNA database were established from 6.5 % of all sampled stone surfaces. For comparison, retrospective casework data analysis from routine crime scene samples demonstrates a success rate of 20.6 % for the establishment of CODIS-suitable DNA profiles from stones sampled for touch DNA. We further investigated how climatic conditions, location and properties of the stones affected the quantity and quality of the recovered DNA. In this study, we show that the quantity of the measurable DNA decreases significantly with increasing temperature. Furthermore, less DNA could be recovered from porous stones, compared to smooth ones

Efficient DNA Sampling in Burglary Investigations

In terms of crime scene investigations by means of forensic DNA-analyses, burglaries are the number one mass crime in Switzerland. Around one third of the DNA trace profiles registered in the Swiss DNA database are related to burglaries. However, during the collection of potential DNA traces within someone’s residence after a burglary, it is not known whether the sampled DNA originated from the perpetrator or from an inhabitant of said home. Because of the high incidence of burglaries, crime scene investigators usually do not collect reference samples from all the residents for economical and administrative reasons. Therefore, the presumably high probability that a DNA profile belonging to a person authorized to be at the crime scene ends up being sent to a DNA database for comparison, has to be taken into account. To our knowledge, no investigation has been made to evaluate the percentage of these non-perpetrator profiles straying into DNA databases. To shed light on this question, we collected reference samples from residents who had been victims of recent burglaries in their private homes. By comparing the profiles established from these reference samples with the profiles generated from trace DNA, we can show that the majority of the DNA samples collected in burglary investigations belong to the residents. Despite the limited number of cases included in the study, presumably due to a crime decline caused by the pandemic, we further show that trace DNA collection in the vicinity of the break and entry area, in particular window and door glasses, is most promising for sampling perpetrator instead of inhabitant DNA

Discovery and characterization of plastic subpopulations associated with distinct hallmarks of cancer in the NSCLC cell line A549

Lung cancer is the leading cause of cancer-related mortality worldwide and is responsible for more than 1 million deaths each year. Despite enormous efforts put in the development of novel treatment strategies, the 5-year survival rate for patients diagnosed with non-small cell lung cancer (NSCLC) remains very low. This is partly due to the difficulty in detecting the disease at early an therefore better treatable time points, which leads to the diagnosis of already locally advanced NSCLC in one-third of the patients. For these patients, concurrent chemo- and/or radiotherapy are considered as standard therapies. The other cause leading to poor survival rate is proposed to lay within the potential of certain tumor cells to resist common treatment strategies and to promote tumor re-initiation, resulting in disease relapse. Up to date, these particular tumor cells have accumulated a variety of characteristic denominations, such as tumor-initiating and tumor-propagating cells, chemoresistant and therefore also tumor- reinitiating cells, as well as metastasizing cells. The most widely used term, which combines all these attributes and features, is cancer stem cell (CSC). Within the first 2 years of my PhD we focused on commonly used treatment strategies for NSCLC and attempted to optimize the gold standard therapy, consisting of pemetrexed and cisplatin, recently recommended for adenocarcinoma lung cancer patients. We demonstrated that the anti-cancer effect of the combination chemotherapy could be enhanced in a schedule- dependent manner. Compared to the simultaneous exposure, called concurrent therapy in the clinic, the pretreatment with pemetrexed prior to cisplatin, i.e. sequential treatment, improved the combination therapy’s efficiency in vitro and provides evidence for the adaptation of the treatment strategy in clinical settings. The follow up project consisted in extrapolating the observed findings to chemo-radiotherapy. Indeed, the pretreatment with pemetrexed prior to ionizing radiation, also optimized the anticancer treatment modality. The second project was initiated after the detection of phenotypically distinct cell and co- lony morphologies within the adenocarcinoma cell line A549 used in the treatment optimization studies. We established relatively stable cultures of three distinct subpopulations, termed holo-, mero- and paraclonal, starting with the isolation of single colonies from the parental popula- tion. We were able to specifically connect phenotype with differential expression profiles and to further attribute distinct hall marks of cancer, i.e. stemness, tumor initiation, treatment resistance, migration/invasion, to the different subpopulations. Holoclone cells are characteri- zed by an epithelial and stem-like phenotype and feature highest tumor-initiation potential. In contrast, paraclone cells exhibit a mesenchymal phenotype, resulting from the activation of epithelial-mesenchymal transition, possess migration and invasion potential and are more tolerant to chemo and IR treatment. Meroclone cells feature intermediate phenotype and gene expression signature. We further demonstrate high degree of plasticity among the phenotypes. In summary, we demonstrate that the cell line A549 consists of subpopulations of cells residing in distinct but dynamic phenotypic states, to which functional properties can be attributed. The model might allow the study of non-genetically dictated processes, such as the epithelial- mesenchymal transition and dedifferentiation, and could evoke a potential adaptation of the classical CSC theory

Efficient DNA Sampling in Burglary Investigations.

In terms of crime scene investigations by means of forensic DNA-analyses, burglaries are the number one mass crime in Switzerland. Around one third of the DNA trace profiles registered in the Swiss DNA database are related to burglaries. However, during the collection of potential DNA traces within someone's residence after a burglary, it is not known whether the sampled DNA originated from the perpetrator or from an inhabitant of said home. Because of the high incidence of burglaries, crime scene investigators usually do not collect reference samples from all the residents for economical and administrative reasons. Therefore, the presumably high probability that a DNA profile belonging to a person authorized to be at the crime scene ends up being sent to a DNA database for comparison, has to be taken into account. To our knowledge, no investigation has been made to evaluate the percentage of these non-perpetrator profiles straying into DNA databases. To shed light on this question, we collected reference samples from residents who had been victims of recent burglaries in their private homes. By comparing the profiles established from these reference samples with the profiles generated from trace DNA, we can show that the majority of the DNA samples collected in burglary investigations belong to the residents. Despite the limited number of cases included in the study, presumably due to a crime decline caused by the pandemic, we further show that trace DNA collection in the vicinity of the break and entry area, in particular window and door glasses, is most promising for sampling perpetrator instead of inhabitant DNA

Tumor Initiation Capacity and Therapy Resistance Are Differential Features of EMT-Related Subpopulations in the NSCLC Cell Line A549

Cell lines are essential tools to standardize and compare experimental findings in basic and translational cancer research. The current dogma states that cancer stem cells feature an increased tumor initiation capacity and are also chemoresistant. Here, we identified and comprehensively characterized three morphologically distinct cellular subtypes in the non–small cell lung cancer cell line A549 and challenge the current cancer stem cell dogma. Subtype-specific cellular morphology is maintained during short-term culturing, resulting in the formation of holoclonal, meroclonal, and paraclonal colonies. A549 holoclone cells were characterized by an epithelial and stem-like phenotype, paraclone cells featured a mesenchymal phenotype, whereas meroclone cells were phenotypically intermediate. Cell-surface marker expression of subpopulations changed over time, indicating an active epithelial-to-mesenchymal transition (EMT), in vitro and in vivo. EMT has been associated with the overexpression of the immunomodulators PD-L1 and PD-L2, which were 37- and 235-fold overexpressed in para- versus holoclone cells, respectively. We found that DNA methylation is involved in epigenetic regulation of marker expression. Holoclone cells were extremely sensitive to cisplatin and radiotherapy in vitro, whereas paraclone cells were highly resistant. However, inhibition of the receptor tyrosine kinase AXL, whose expression is associated with an EMT, specifically targeted the otherwise highly resistant paraclone cells. Xenograft tumor formation capacity was 24- and 269-fold higher in holo- than mero- and paraclone cells, respectively. Our results show that A549 subpopulations might serve as a unique system to explore the network of stemness, cellular plasticity, tumor initiation capacity, invasive and metastatic potential, and chemo/radiotherapy resistance